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Coding Skills

R
Python
Bash
AWK
SQL
Perl

Languages

Polish
English
French
Estonian

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Made with the R package pagedown.

Based on the Nick Strayer’s CV package; modified source code for this CV is available here.

Last updated on 2022-09-30.

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Kasia Kedzierska

I am a PhD student at the University of Oxford. As a computational biologist, I use Data Science and Machine Learning to answer biological questions. Specifically, I study cancer of the uterus and chromatin organisation in disease progression. Last summer, I joined Computational Biology Department at Novo Nordisk Research Centre in Oxford as an intern, where I was working with NLP methods and knowledge graphs. Currently, I am looking into adapting my experience from the internship to build models for investigating cancer evolution.

Research Experience

Intern

Novo Nordisk Research Centre Oxford

Oxford, United Kingdom

2021

  • I used NLP based methods to screen biomedical artciles and identify potential therapeutic targets. I built R Shiny App to allow colleagues within the company to investigate results from our pipeline.

DPhil Candidate

Wellcome Centre for Human Genetics, Big Data Institute

University of Oxford, UK

present - 2018

  • In my PhD project Functional and evolutionary characterisation of chromatin organisation in endometrial cancer I am looking at how chromatin organisation influences disease progression in cancer of the uterus.
  • Mentored by D. Church and D. Woodcock
  • Currently I’m working on building and refining ML models of cancer evolution.

Visiting Graduate Student

Ratan group

University of Virginia, USA

2018 - 2017

  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
  • Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.

Visiting Graduate Student

Pemberton group

University of Virginia, USA

2017 - 2016

  • Worked on Epigenetic regulation in prostate cancer.
  • Performed experiments and analyzed data from RNA-seq, ATAC-seq, and ChIP-seq assays.

Research Assistant

Zebrafish Developmental Genomics

IIMCB, Warsaw, Poland

2016 - 2015

  • I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
  • I was responsible for both computational and experimental aspects of the project.

Education

DPhil. Candidate, Genomic Medicine and Statistics

Nuffield Department of Medicine, Brasenose College

University of Oxford, UK

present - 2018

M. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2018 - 2015

  • Master thesis: - Analysis of the mutational burden across gene sets in cancer awarded the title of The Best Master Thesis in Bioinformatics defended in 2018.

B. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2015 - 2011

Publications

Discordant prognosis of mismatch repair deficiency in colorectal and endometrial cancer reflects variation in antitumour immune response and immune escape

Mark A Glaire, Neil AJ Ryan, Marieke E Ijsselsteijn, Katarzyna Kedzierska, Sofia Obolenski, Reem Ali, Emma J Crosbie, Tjalling Bosse, Noel Fcc De Miranda, David N Church

The Journal of pathology

2022

Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift

M. Migdal, E. Tralle, K. A. Nahia, L. Bugajski, K. Z. Kedzierska, F. Garbicz, K. Piwocka, C. L. Winata, M. Pawlak

BMC Genomics

2021

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

H. Russell, K. Kedzierska, D. D. Buchanan, R. Thomas, E. Tham, M. Mints, A. Keränen, G. G. Giles, M. C. Southey, R. L. Milne, I. Tomlinson, D. Church, A. B. Spurdle, T. A. O’Mara and A. Lewis

Clinical Epigenetics

2020

Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer

N. Horeweg, M. de Bruyn, R. A. Nout, E. Stelloo, K. Kedzierska, A. León-Castillo, A. Plat, K. D. Mertz, M. Osse, I. M. Jürgenliemk-Schulz, L. C.H.W. Lutgens, J. J. Jobsen, E. M. van der Steen-Banasik, V. T. Smit, C. L. Creutzberg, T. Bosse, H. W. Nijman, V. H. Koelzer and D. N. Church

Cancer Immunology Research

2020

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

M. Pawlak, K. Z. Kedzierska, M. Migdal, K. A. Nahia, J. A. Ramilowski, L. Bugajski, K. Hashimoto, A. Marconi, K. Piwocka, P. Carninci and C. L. Winata

Genome Research

2019

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

K. Jividen, K. Z. Kedzierska, C.-S. Yang, K. Szlachta, A. Ratan and B. M. Paschal

BMC Cancer

2018

SONiCS: PCR stutter noise correction in genome-scale microsatellites

K. Z. Kedzierska, L. Gerber, D. Cagnazzi, M. Krützen, A. Ratan, L. Kistler

Bioinformatics

2018

Posters, and Talks

Systematic characterisation of chromatin modifiers in endometrial cancer

European Association for Cancer Research 2022 Congress

Seville, Spain

2022

Analysis of the mutational burden across gene sets in cancer

Polish Bioinformatics Society Symposium

Cracow, Poland

2019

  • Invited talk

Differential mutation analysis across gene sets in cancers

Biology of Genomes 2018

Cold Spring Harbor, NY, USA

2018

  • Poster

Epigenetic regulation of prostate cancer

Visiting Graduate Traineeship Program Grantees Symposium

Charlottesville, VA, USA

2017

  • Talk

Awards and honours

Senior Hulme Scholarship

Brasenose College, University of Oxford

Oxford, UK

present - 2021

  • Senior Hulme Scholarship is awarded by Brasenose College, University of Oxford to DPhil students whose academic performance is deemed to be exceptional.

Graduate Prize in the ‘Outstanding work outside degree’ category

Nuffield Department of Medicine, University of Oxford

Oxford, UK

2022 - 2021

  • Each year Nuffield Department of Medicine, based on nominations, awards selected PhD students based on their performance within and outside of their degree.

Best Master Thesis in Bioinformatics       

Polish Bioinformatics Society

Poland

2019 - 2018

  • Analysis of the mutational burden across gene sets in cancer - Best Master Thesis defended in Bioinformatics in 2018 in Poland.

Visiting Graduate Traineeship Program, now known as BioLAB

Fulbright Poland

University of Virginia, VA, USA

2017 - 2016

  • The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.

Grasz o Staz

PwC Poland

Poland

2015

  • “Grasz o Staz” competition was a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.

Teaching Experience

Unsupervised learning

NGSchool2022: Machine Learning in Computational Biology

Jablonna, Poland

2022

Data visualization in bioinformatics - hackathon mentor

Online hackathon NGSprint

Discord

2021

  • I led the hackathon in data viusalisation with emphasis on computational biology. Under my supervision, 3 teams of around 5 people each, created interactive and captivating visualisation. Teaching materials are available at github.com/kzkedzierska/NGSprint_data_viz.

Online tutorials: Python for Data Science and Introduction to Python

NGSeminars

YouTube

2020

Unsupervised learning, Introduction to Python

#NGSchool2019: Machine Learning for Biomedicine

Ostróda, Poland

2019

  • Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
  • Materials for the Introduction to Python are available on github

Introduction to R

Wellcome Centre for Human Genetics

Oxford, United Kingdom

2019

  • 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
  • Materials available on github/kzkedziersa/r_intro

Introduction to Managing Code with Git

Wellcome Centre for Human Genetics

Oxford, United Kingdom

2020 - 2019

ATAC-seq workshop

#NGSchool2017: Single-cell Sequencing

Jachranka, Poland

2017

Attended Workshops, Summer Schools

Machine Learning Summer School

Imperial College London, University College London

London, United Kingdom

2019

Grants

Visegrad Grant to organize #NGSchool2020 postponed until 2022

Visegrad Fund

N/A

2022 - 2020

  • 32,190 EUR awarded towards organising affordable training and conference focusing on ML application in Computational Biology. During this project I managed an international team of 9 people and led the organisation of summer school, conference, online seminars and hackathon.

Visegrad Grant to organize #NGSchool2019

Visegrad Fund

N/A

2019

  • 23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.

Non profit work

President

NGSchool Society

N/A

2022 - 2018

  • The goal of the Society is to promote and support science, with emphasis on computational biology.
  • President since 2019; Vice President 2018 - 2019, Founder